Genome‐wide characterization and developmental expression profiling of long non‐coding RNAs in <i>Sogatella furcifera</i>

Chang, Zhaoxia; Ajayi, Olugbenga Emmanuel; Guo, Dongyang; Wu, Qingfa

doi:10.1111/1744-7917.12707

Cited by 26 publications

(28 citation statements)

References 59 publications

(77 reference statements)

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“…The lncRNAs are responsible for several key physiological processes [32,33], including epigenetics [34], immune response [35], and protein degradation [36]. LncRNAs in insect species have now been studied in D. melanogaster [5], A. aegypti [24], B. mori [26], P. xylostella [19], N. lugens [1], and Phlebotomus perniciosus [37].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide analysis of long non-coding RNAs in adult tissues of the melon fly, Zeugodacus cucurbitae (Coquillett)

Song

Han

et al. 2020

BMC Genomics

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Background: Long non-coding RNAs (lncRNAs) are involved in many fundamental biological processes, such as transcription regulation, protein degradation, and cell differentiation. Information on lncRNA in the melon fly, Zeugodacus cucurbitae (Coquillett) is currently limited. Results: We constructed 24 RNA-seq libraries from eight tissues (midgut, Malpighian tubules, fat body, ovary, and testis) of Z. cucurbitae adults. A total of 3124 lncRNA transcripts were identified. Among those, 1464 were lincRNAs, 1037 were intronic lncRNAs, 301 were anti-sense lncRNAs, and 322 were sense lncRNAs. The majority of lncRNAs contained two exons and one isoform. Differentially expressed lncRNAs were analyzed between tissues, and Malpighian tubules versus testis had the largest number. Some lncRNAs exhibited strong tissue specificity. Specifically expressed lncRNAs were identified and filtered in tissues of female and male Z. cucurbitae based on their expression levels. Four midgut-specific lncRNAs were validated by quantitative real-time polymerase chain reaction (RT-qPCR), and the data were consistent with RNA-seq data. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of targets of midgut-specific lncRNAs indicated an enrichment of the metabolic process. Conclusions: This was the first systematic identification of lncRNA in the melon fly. Expressions of lncRNAs in multiple adult tissues were evaluated by quantitative transcriptomic analysis. These qualitative and quantitative analyses of lncRNAs, especially the tissue-specific lncRNAs in Z. cucurbitae, provide useful data for further functional studies.

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Section: Discussionmentioning

confidence: 99%

Genome-wide analysis of long non-coding RNAs in adult tissues of the melon fly, Zeugodacus cucurbitae (Coquillett)

Song

Han

et al. 2020

BMC Genomics

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“…With the help of NGS, genomes of all three planthoppers were sequenced, resulting in the identification of many functional genes [ 143 , 144 , 145 ]. From this study, 2439 lncRNA transcripts were reported in BPH [ 146 ], 5790 lncRNA transcripts were identified in SBPH [ 147 ], and 1852 lncRNA transcripts were found in WBPH [ 148 ]. Interestingly, these lncRNAs from different insects shared similar sequences due to their close genetic relationships.…”

Section: Identification and Functional Characterization Of Lncrnasmentioning

confidence: 99%

Long Non-Coding RNAs in Insects

Choudhary

Sharma

Meghwanshi

et al. 2021

Animals

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Only a small subset of all the transcribed RNAs are used as a template for protein translation, whereas RNA molecules that are not translated play a very important role as regulatory non-coding RNAs (ncRNAs). Besides traditionally known RNAs (ribosomal and transfer RNAs), ncRNAs also include small non-coding RNAs (sncRNAs) and long non-coding RNAs (lncRNAs). The lncRNAs, which were initially thought to be junk, have gained a great deal attention because of their regulatory roles in diverse biological processes in animals and plants. Insects are the most abundant and diverse group of animals on this planet. Recent studies have demonstrated the role of lncRNAs in almost all aspects of insect development, reproduction, and genetic plasticity. In this review, we describe the function and molecular mechanisms of the mode of action of different insect lncRNAs discovered up to date.

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“…Recently, we assembled two chromosome-scale genomes of male and female FAW from China with superior quality compared with other FAW assemblies reported to date (Gui et al, 2020). A series of transcriptome data sets was produced across various strains and treatments (Landais et al, 2003;Legeai et al, 2014;Kakumani et al, 2015;do Nascimento et al, 2015;Silva-Brandao et al, 2017;Orsucci et al, 2018;Chang et al, 2020). Further processing of these omics data will generate more functional information of genes, such as Gene Ontology and pathways annotations, orthologous gene relationships between FAW and other model species (Sullivan et al, 2013), co-expression networks (Langfelder & Horvath, 2008), and interolog-based protein-protein interaction (PPI) network (Matthews et al, 2001).…”

Section: Introductionmentioning

confidence: 99%

FAWMine: An integrated database and analysis platform for fall armyworm genomics

et al. 2021

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Fall armyworm (Spodoptera frugiperda), a native insect species in the Americas, is rapidly becoming a major agricultural pest worldwide and is causing great damage to corn, rice, soybeans, and other crops. To control this pest, scientists have accumulated a great deal of high-throughput data of fall armyworm, and nine versions of its genomes and transcriptomes have been published. However, easily accessing and performing integrated analysis of these omics data sets is challenging. Here, we developed the Fall Armyworm Genome Database (FAWMine, http://159.226.67.243:8080/fawmine/) to maintain genome sequences, structural and functional annotations, transcriptomes, co-expression, protein interactions, homologs, pathways, and single-nucleotide variations. FAWMine provides a powerful framework that helps users to perform flexible and customized searching, present integrated data sets using diverse visualization methods, output results tables in a range of file formats, analyze candidate gene lists using multiple widgets, and query data available in other InterMine systems. Additionally, stand-alone JBrowse and BLAST services are also established, allowing the users to visualize RNA-Seq data and search genome and annotated gene sequences. Altogether, FAWMine is a useful tool for querying, visualizing, and analyzing compiled data sets rapidly and efficiently. FAWMine will be continually updated to function as a community resource for fall armyworm genomics and pest control research.

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Genome‐wide characterization and developmental expression profiling of long non‐coding RNAs in Sogatella furcifera

Cited by 26 publications

References 59 publications

Genome-wide analysis of long non-coding RNAs in adult tissues of the melon fly, Zeugodacus cucurbitae (Coquillett)

Genome-wide analysis of long non-coding RNAs in adult tissues of the melon fly, Zeugodacus cucurbitae (Coquillett)

Long Non-Coding RNAs in Insects

FAWMine: An integrated database and analysis platform for fall armyworm genomics

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